Conformational studies of the backbone (poly- N-acetyllactosamine) and the core region sequences of O-linked carbohydrate chains

The AMBER forcefield with added carbohydrate specific parameters for potential types, charges and anomericity has been used to explore the conformational space sampled by oligosaccharides of repeating (Galβ1-4GlcNAcβ1-3) n sequence and those having α chain terminating substituents on a Galβ1-3GalN Acα, O-glycosylated core. The 17 lowest energy forms of the 16-mer N-acetyllactosaminic sequence included fully extended units and spring-like coils with dielectric constant 80 to simulate a water environment. More restricted stereochemistry was exhibited by the glycosylation adjacent to the core as has been previously predicted by n.m.r. studies.